Microbiome Analyses

Sample Data Characteristics

16242416HPV-/BV-HPV-/BV+HPV+/BV-HPV+/BV+0510152025
HPV-/BV-HPV-/BV+HPV+/BV-HPV+/BV+hpv_bvn
8270AsianHispanic/LatinaNon_Hispanic010203040506070
AsianHispanic/LatinaNon_Hispanicethnicityn

Relative Abundance Plots at the grouped and independent level of samples

hpv_bv00.20.40.60.81
LactobacillusGardnerellaShuttleworthiaMegasphaeraPrevotellaSneathiaAtopobiumNot_AssignedStreptococcusMobiluncusDialisterParvimonasClostridiumAerococcusAnaerococcusStreptobacillusVeillonellaArcanobacteriumPeptoniphilusMycoplasmaPeptostreptococcusStaphylococcusMoryellaPorphyromonasFusobacteriumGemellaUreaplasmaBifidobacteriumFinegoldiaEnterococcusCorynebacteriumSutterellaBulleidiaBacteroidesCampylobacterRuminococcusPeptococcusHaemophilusSlackiaVaribaculumBlautiaChlamydiaMicrococcusAcinetobacterJanthinobacteriumGranulicatellaWAL_1855DPropionibacteriumCF231Parabacteroides1_68FlavobacteriumOscillospira
hpv_bv00.20.40.60.81
LactobacillusGardnerellaShuttleworthiaMegasphaeraPrevotellaSneathiaAtopobiumNot_AssignedStreptococcusDialisterMobiluncusParvimonasClostridiumAerococcusAnaerococcusStreptobacillusArcanobacteriumPeptoniphilusMycoplasmaVeillonellaPeptostreptococcusStaphylococcusMoryellaPorphyromonasFusobacteriumBifidobacteriumGemellaUreaplasmaFinegoldiaSutterellaEnterococcusBulleidiaCorynebacteriumBacteroidesCampylobacterRuminococcusPeptococcusHaemophilusVaribaculumSlackiaBlautiaChlamydiaMicrococcusAcinetobacterJanthinobacteriumGranulicatellaWAL_1855DPropionibacteriumCF231Parabacteroides1_68FlavobacteriumOscillospira
hpv00.20.40.60.81
LactobacillusGardnerellaShuttleworthiaMegasphaeraPrevotellaSneathiaAtopobiumNot_AssignedStreptococcusDialisterMobiluncusParvimonasClostridiumAerococcusAnaerococcusStreptobacillusArcanobacteriumPeptoniphilusMycoplasmaVeillonellaPeptostreptococcusStaphylococcusMoryellaPorphyromonasFusobacteriumBifidobacteriumGemellaUreaplasmaFinegoldiaSutterellaEnterococcusBulleidiaCorynebacteriumBacteroidesCampylobacterRuminococcusPeptococcusHaemophilusVaribaculumSlackiaBlautiaChlamydiaMicrococcusAcinetobacterJanthinobacteriumGranulicatellaWAL_1855DPropionibacteriumCF231Parabacteroides1_68FlavobacteriumOscillospira
hpv00.20.40.60.81
LactobacillusGardnerellaShuttleworthiaMegasphaeraPrevotellaSneathiaAtopobiumNot_AssignedStreptococcusDialisterMobiluncusParvimonasClostridiumAerococcusAnaerococcusStreptobacillusArcanobacteriumPeptoniphilusMycoplasmaVeillonellaPeptostreptococcusStaphylococcusMoryellaPorphyromonasFusobacteriumBifidobacteriumGemellaUreaplasmaFinegoldiaSutterellaEnterococcusBulleidiaCorynebacteriumBacteroidesCampylobacterRuminococcusPeptococcusHaemophilusVaribaculumSlackiaBlautiaChlamydiaMicrococcusAcinetobacterJanthinobacteriumGranulicatellaWAL_1855DPropionibacteriumCF231Parabacteroides1_68FlavobacteriumOscillospira
bv00.20.40.60.81
LactobacillusGardnerellaShuttleworthiaMegasphaeraPrevotellaSneathiaAtopobiumNot_AssignedStreptococcusDialisterMobiluncusParvimonasClostridiumAerococcusAnaerococcusStreptobacillusArcanobacteriumPeptoniphilusMycoplasmaVeillonellaPeptostreptococcusStaphylococcusMoryellaPorphyromonasFusobacteriumBifidobacteriumGemellaUreaplasmaFinegoldiaSutterellaEnterococcusBulleidiaCorynebacteriumBacteroidesCampylobacterRuminococcusPeptococcusHaemophilusVaribaculumSlackiaBlautiaChlamydiaMicrococcusAcinetobacterJanthinobacteriumGranulicatellaWAL_1855DPropionibacteriumCF231Parabacteroides1_68FlavobacteriumOscillospira
bv00.20.40.60.81
LactobacillusGardnerellaShuttleworthiaMegasphaeraPrevotellaSneathiaAtopobiumNot_AssignedStreptococcusDialisterMobiluncusParvimonasClostridiumAerococcusAnaerococcusStreptobacillusArcanobacteriumPeptoniphilusMycoplasmaVeillonellaPeptostreptococcusStaphylococcusMoryellaPorphyromonasFusobacteriumBifidobacteriumGemellaUreaplasmaFinegoldiaSutterellaEnterococcusBulleidiaCorynebacteriumBacteroidesCampylobacterRuminococcusPeptococcusHaemophilusVaribaculumSlackiaBlautiaChlamydiaMicrococcusAcinetobacterJanthinobacteriumGranulicatellaWAL_1855DPropionibacteriumCF231Parabacteroides1_68FlavobacteriumOscillospira
race00.20.40.60.81
LactobacillusGardnerellaShuttleworthiaMegasphaeraSneathiaPrevotellaAtopobiumNot_AssignedParvimonasDialisterMobiluncusStreptococcusClostridiumAerococcusAnaerococcusPeptoniphilusPeptostreptococcusStreptobacillusVeillonellaArcanobacteriumMycoplasmaFinegoldiaPorphyromonasStaphylococcusGemellaMoryellaUreaplasmaFusobacteriumBifidobacteriumCorynebacteriumSutterellaBulleidiaEnterococcusVaribaculumRuminococcusBacteroidesSlackiaCampylobacterPeptococcusHaemophilusBlautiaAcinetobacterMicrococcusJanthinobacteriumChlamydiaWAL_1855D1_68PropionibacteriumCF231GranulicatellaParabacteroidesFlavobacteriumOscillospira
race00.20.40.60.81
LactobacillusGardnerellaShuttleworthiaMegasphaeraPrevotellaSneathiaAtopobiumNot_AssignedStreptococcusDialisterMobiluncusParvimonasClostridiumAerococcusAnaerococcusStreptobacillusArcanobacteriumPeptoniphilusMycoplasmaVeillonellaPeptostreptococcusStaphylococcusMoryellaPorphyromonasFusobacteriumBifidobacteriumGemellaUreaplasmaFinegoldiaSutterellaEnterococcusBulleidiaCorynebacteriumBacteroidesCampylobacterRuminococcusPeptococcusHaemophilusVaribaculumSlackiaBlautiaChlamydiaMicrococcusAcinetobacterJanthinobacteriumGranulicatellaWAL_1855DPropionibacteriumCF231Parabacteroides1_68FlavobacteriumOscillospira

Relative Abundance Comparison Plots at genus level

HPV+/-

LactobacillusGardnerellaShuttleworthiaAtopobium0123456
HPV-HPV+logcpm

BV+/-

LactobacillusGardnerellaShuttleworthiaAtopobium00.20.40.60.81
BV-BV+relative abundance

HPV+/-/BV+/-

LactobacillusGardnerellaShuttleworthiaAtopobium00.20.40.60.81
HPV-/BV-HPV-/BV+HPV+/BV-HPV+/BV+relative abundance

Alpha diversity plots

HPV/BV

HPV-/BV-HPV-/BV+HPV+/BV-HPV+/BV+0.00.51.01.52.0
conditionHPV-/BV-HPV-/BV+HPV+/BV-HPV+/BV+Alpha diversity between hpv_bv (shannon)conditionshannon
                              output
Method  Kruskal-Wallis rank sum test
P-value         0.000155114715447703

HPV

HPV-HPV+0.00.51.01.52.0
conditionHPV-HPV+Alpha diversity between hpv (shannon)conditionshannon
        Wilcoxon rank sum exact test Welch Two Sample t-test
P-value                    0.9047971               0.9263054

BV

BV-BV+0.00.51.01.52.0
conditionBV-BV+Alpha diversity between bv (shannon)conditionshannon
        Wilcoxon rank sum exact test Welch Two Sample t-test
P-value                 8.936951e-06            6.763516e-06

Beta Diversity

HPV/BV

HPV

BV

Taxonomic Trees

Differential Abundance